Re: [Rdkit-discuss] updating the rdkit project on sourceforge
Here is, hopefully, the last update on this topic. Apologies for the verbosity. One unfortunate thing about this update is that the svn repository has moved. If you have a version of the source checked out via svn, you need to change the repository URL. You have a few choices: 1) checkout a fresh copy (instructions for how to do that are here: http://sourceforge.net/p/rdkit/code) 2) switch your existing copy. The method for the switch depends on how you checked out the code in the first place, but this is what I just did : svn switch --username glandrum --relocate https://rdkit.svn.sourceforge.net/svnroot/rdkit/trunk https://svn.code.sf.net/p/rdkit/code/trunk I'm not quite sure why, but this worked for me on linux, but not on the Mac. 3) If you have unchecked-in changes that you want to keep, you can do something like this: - cd $RDBASE - svn update - cd .. - svn diff $RDBASE rdk.patch - mv $RDBASE $RDBASE.old - do a fresh rdkit checkout as directed in option 1 above, make sure it goes into the directory $RDBASE - patch -p0 ./rdk.patch Best, -greg On Fri, Aug 17, 2012 at 8:25 AM, Greg Landrum greg.land...@gmail.com wrote: Ok, the change I mentioned below has been made; we're now using the new sourceforge tools. I've update the links on www.rdkit.org. The svn migration is still ongoing, so at the moment svn is unavailable. Once the migration is complete, people who are using the RDKit svn repository will need to change their local copies. I'll send information about how to do this once the migration has finished. -greg On Thu, Aug 16, 2012 at 5:24 AM, Greg Landrum greg.land...@gmail.com wrote: Dear all, Sourceforge has new backend software that they are encouraging everyone to switch their projects too. Based on the descriptions (https://sourceforge.net/p/allura/wiki/Features/) it sounds like a good idea to me, so I plan to go ahead and initiate the update in the next couple of days (unless one of you has a strong opinion that it would be a bad idea). Aside from a more modern web experience and the new features described above, the only real significant change that you should see is that the URLs for the svn repository will change. I will send updated info about this after the switch (when I know the new urls). For those interested, there are some details about the upgrade process here: https://sourceforge.net/p/upgrade/ Best, -greg -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] RDKit ctest failed
Dear colleagues, after compiling and installing last RDKit under Ubuntu12.04 (64bit) I have following test failed. The following tests FAILED: 3 - pyBV (Failed) 8 - testPyGeometry (Failed) 35 - pyChemReactions (Failed) 42 - pyMolDescriptors (Failed) 61 - pyGraphMolWrap (SEGFAULT) 69 - pyFeatures (Failed) 76 - pythonTestDirChem (Failed) I can't find the source of mistakes and errors. Can you please suggest me any solutions? RDBASE is provided in .bashrc, boost and openbabel library are installed in default Ubuntu paths. Thank you, -- Vladimir Chupakhin, Boston, MA, USA LinkedIN: http://www.linkedin.com/in/chupvl *Info from the log file* 3/76 Testing: pyBV 3/76 Test: pyBV Command: /usr/bin/python /home/chupvl/scisoft/rdkit/Code/DataStructs/Wrap/testBV.py Directory: /home/chupvl/scisoft/rdkit/build/Code/DataStructs/Wrap pyBV start time: Aug 17 10:38 EDT Output: -- ...EE == ERROR: test7FPS (__main__.TestCase) -- Traceback (most recent call last): File /home/chupvl/scisoft/rdkit/Code/DataStructs/Wrap/testBV.py, line 153, in test7FPS self.failUnlessEqual(DataStructs.BitVectToFPSText(bv),03008280) AttributeError: 'module' object has no attribute 'BitVectToFPSText' 8/76 Testing: testPyGeometry 8/76 Test: testPyGeometry Command: /usr/bin/python /home/chupvl/scisoft/rdkit/Code/Geometry/Wrap/testGeometry.py Directory: /home/chupvl/scisoft/rdkit/build/Code/Geometry/Wrap testPyGeometry start time: Aug 17 10:38 EDT Output: -- ..E.. == ERROR: test6Dihedrals (__main__.TestCase) -- Traceback (most recent call last): File /home/chupvl/scisoft/rdkit/Code/Geometry/Wrap/testGeometry.py, line 350, in test6Dihedrals ang = geom.ComputeDihedralAngle(p1,p2,p3,p4) AttributeError: 'module' object has no attribute 'ComputeDihedralAngle' -- Ran 9 tests in 0.023s FAILED (errors=1) Testing Geometry wrapper end of output Test time = 0.08 sec -- Test Failed. testPyGeometry end time: Aug 17 10:38 EDT testPyGeometry time elapsed: 00:00:00 -- 35/76 Testing: pyChemReactions 35/76 Test: pyChemReactions Command: /usr/bin/python /home/chupvl/scisoft/rdkit/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py Directory: /home/chupvl/scisoft/rdkit/build/Code/GraphMol/ChemReactions/Wrap pyChemReactions start time: Aug 17 10:38 EDT Output: -- ..E...[10:38:56] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])Q [10:38:56] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])[N:3]Q .[10:38:56] reactant atom-mapping number 1 found multiple times. [10:38:56] product atom-mapping number 2 not found in reactants. F.E. == ERROR: test16GetReactingAtoms (__main__.TestCase) -- Traceback (most recent call last): File /home/chupvl/scisoft/rdkit/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py, line 399, in test16GetReactingAtoms rAs = rxn.GetReactingAtoms() AttributeError: 'ChemicalReaction' object has no attribute 'GetReactingAtoms' == ERROR: test8Properties (__main__.TestCase) -- Traceback (most recent call last): File /home/chupvl/scisoft/rdkit/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py, line 286, in test8Properties self.failUnlessEqual(ps[0][0].GetAtomWithIdx(1).GetIsotope(),3); AttributeError: 'Atom' object has no attribute 'GetIsotope' == FAIL: test5Validation (__main__.TestCase) -- Traceback (most recent call last): File /home/chupvl/scisoft/rdkit/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py, line 250, in test5Validation self.failUnless(rxn.Validate()==(1,1)) AssertionError: False is not true -- Ran 15 tests in 0.008s FAILED (failures=1, errors=2) end of output Test time = 0.10 sec -- Test Failed. pyChemReactions end time: Aug 17 10:38 EDT pyChemReactions time elapsed: 00:00:00 -- 42/76 Testing: pyMolDescriptors 42/76 Test: pyMolDescriptors
Re: [Rdkit-discuss] RDKit ctest failed
Dear Vladimir, Check the python path . RDBASE must have the python path. Abhik Seal Indiana University Bloomington Department of Chemical Informatics abs...@indiana.edu *OSDD CHEMINFORMATICS* +18123699097 http://mypage.iu.edu/~abseal/index.htm On Fri, Aug 17, 2012 at 8:29 PM, Vladimir Chupakhin chu...@gmail.comwrote: Dear colleagues, after compiling and installing last RDKit under Ubuntu12.04 (64bit) I have following test failed. The following tests FAILED: 3 - pyBV (Failed) 8 - testPyGeometry (Failed) 35 - pyChemReactions (Failed) 42 - pyMolDescriptors (Failed) 61 - pyGraphMolWrap (SEGFAULT) 69 - pyFeatures (Failed) 76 - pythonTestDirChem (Failed) I can't find the source of mistakes and errors. Can you please suggest me any solutions? RDBASE is provided in .bashrc, boost and openbabel library are installed in default Ubuntu paths. Thank you, -- Vladimir Chupakhin, Boston, MA, USA LinkedIN: http://www.linkedin.com/in/chupvl *Info from the log file* 3/76 Testing: pyBV 3/76 Test: pyBV Command: /usr/bin/python /home/chupvl/scisoft/rdkit/Code/DataStructs/Wrap/testBV.py Directory: /home/chupvl/scisoft/rdkit/build/Code/DataStructs/Wrap pyBV start time: Aug 17 10:38 EDT Output: -- ...EE == ERROR: test7FPS (__main__.TestCase) -- Traceback (most recent call last): File /home/chupvl/scisoft/rdkit/Code/DataStructs/Wrap/testBV.py, line 153, in test7FPS self.failUnlessEqual(DataStructs.BitVectToFPSText(bv),03008280) AttributeError: 'module' object has no attribute 'BitVectToFPSText' 8/76 Testing: testPyGeometry 8/76 Test: testPyGeometry Command: /usr/bin/python /home/chupvl/scisoft/rdkit/Code/Geometry/Wrap/testGeometry.py Directory: /home/chupvl/scisoft/rdkit/build/Code/Geometry/Wrap testPyGeometry start time: Aug 17 10:38 EDT Output: -- ..E.. == ERROR: test6Dihedrals (__main__.TestCase) -- Traceback (most recent call last): File /home/chupvl/scisoft/rdkit/Code/Geometry/Wrap/testGeometry.py, line 350, in test6Dihedrals ang = geom.ComputeDihedralAngle(p1,p2,p3,p4) AttributeError: 'module' object has no attribute 'ComputeDihedralAngle' -- Ran 9 tests in 0.023s FAILED (errors=1) Testing Geometry wrapper end of output Test time = 0.08 sec -- Test Failed. testPyGeometry end time: Aug 17 10:38 EDT testPyGeometry time elapsed: 00:00:00 -- 35/76 Testing: pyChemReactions 35/76 Test: pyChemReactions Command: /usr/bin/python /home/chupvl/scisoft/rdkit/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py Directory: /home/chupvl/scisoft/rdkit/build/Code/GraphMol/ChemReactions/Wrap pyChemReactions start time: Aug 17 10:38 EDT Output: -- ..E...[10:38:56] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])Q [10:38:56] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])[N:3]Q .[10:38:56] reactant atom-mapping number 1 found multiple times. [10:38:56] product atom-mapping number 2 not found in reactants. F.E. == ERROR: test16GetReactingAtoms (__main__.TestCase) -- Traceback (most recent call last): File /home/chupvl/scisoft/rdkit/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py, line 399, in test16GetReactingAtoms rAs = rxn.GetReactingAtoms() AttributeError: 'ChemicalReaction' object has no attribute 'GetReactingAtoms' == ERROR: test8Properties (__main__.TestCase) -- Traceback (most recent call last): File /home/chupvl/scisoft/rdkit/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py, line 286, in test8Properties self.failUnlessEqual(ps[0][0].GetAtomWithIdx(1).GetIsotope(),3); AttributeError: 'Atom' object has no attribute 'GetIsotope' == FAIL: test5Validation (__main__.TestCase) -- Traceback (most recent call last): File /home/chupvl/scisoft/rdkit/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py, line 250, in test5Validation self.failUnless(rxn.Validate()==(1,1)) AssertionError: False is not true
Re: [Rdkit-discuss] RDKit ctest failed
I have added this into the .bashrc export RDBASE=/home/chupvl/scisoft/rdkit/ export PYTHONPATH=/home/chupvl/scisoft/rdkit/:/usr/include/python2.7/ export LD_LIBRARY_PATH=/home/chupvl/scisoft/rdkit/lib/ but actually received even *more* Failed messages. Best regards, -- Vladimir Chupakhin, Boston, MA, USA tel: +1-617-943-9710 LinkedIN: http://www.linkedin.com/in/chupvl On Fri, Aug 17, 2012 at 11:07 AM, Abhik Seal abhik1...@gmail.com wrote: Dear Vladimir, Check the python path . RDBASE must have the python path. Abhik Seal Indiana University Bloomington Department of Chemical Informatics abs...@indiana.edu *OSDD CHEMINFORMATICS* +18123699097 http://mypage.iu.edu/~abseal/index.htm On Fri, Aug 17, 2012 at 8:29 PM, Vladimir Chupakhin chu...@gmail.comwrote: Dear colleagues, after compiling and installing last RDKit under Ubuntu12.04 (64bit) I have following test failed. The following tests FAILED: 3 - pyBV (Failed) 8 - testPyGeometry (Failed) 35 - pyChemReactions (Failed) 42 - pyMolDescriptors (Failed) 61 - pyGraphMolWrap (SEGFAULT) 69 - pyFeatures (Failed) 76 - pythonTestDirChem (Failed) I can't find the source of mistakes and errors. Can you please suggest me any solutions? RDBASE is provided in .bashrc, boost and openbabel library are installed in default Ubuntu paths. Thank you, -- Vladimir Chupakhin, Boston, MA, USA LinkedIN: http://www.linkedin.com/in/chupvl *Info from the log file* 3/76 Testing: pyBV 3/76 Test: pyBV Command: /usr/bin/python /home/chupvl/scisoft/rdkit/Code/DataStructs/Wrap/testBV.py Directory: /home/chupvl/scisoft/rdkit/build/Code/DataStructs/Wrap pyBV start time: Aug 17 10:38 EDT Output: -- ...EE == ERROR: test7FPS (__main__.TestCase) -- Traceback (most recent call last): File /home/chupvl/scisoft/rdkit/Code/DataStructs/Wrap/testBV.py, line 153, in test7FPS self.failUnlessEqual(DataStructs.BitVectToFPSText(bv),03008280) AttributeError: 'module' object has no attribute 'BitVectToFPSText' 8/76 Testing: testPyGeometry 8/76 Test: testPyGeometry Command: /usr/bin/python /home/chupvl/scisoft/rdkit/Code/Geometry/Wrap/testGeometry.py Directory: /home/chupvl/scisoft/rdkit/build/Code/Geometry/Wrap testPyGeometry start time: Aug 17 10:38 EDT Output: -- ..E.. == ERROR: test6Dihedrals (__main__.TestCase) -- Traceback (most recent call last): File /home/chupvl/scisoft/rdkit/Code/Geometry/Wrap/testGeometry.py, line 350, in test6Dihedrals ang = geom.ComputeDihedralAngle(p1,p2,p3,p4) AttributeError: 'module' object has no attribute 'ComputeDihedralAngle' -- Ran 9 tests in 0.023s FAILED (errors=1) Testing Geometry wrapper end of output Test time = 0.08 sec -- Test Failed. testPyGeometry end time: Aug 17 10:38 EDT testPyGeometry time elapsed: 00:00:00 -- 35/76 Testing: pyChemReactions 35/76 Test: pyChemReactions Command: /usr/bin/python /home/chupvl/scisoft/rdkit/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py Directory: /home/chupvl/scisoft/rdkit/build/Code/GraphMol/ChemReactions/Wrap pyChemReactions start time: Aug 17 10:38 EDT Output: -- ..E...[10:38:56] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])Q [10:38:56] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])[N:3]Q .[10:38:56] reactant atom-mapping number 1 found multiple times. [10:38:56] product atom-mapping number 2 not found in reactants. F.E. == ERROR: test16GetReactingAtoms (__main__.TestCase) -- Traceback (most recent call last): File /home/chupvl/scisoft/rdkit/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py, line 399, in test16GetReactingAtoms rAs = rxn.GetReactingAtoms() AttributeError: 'ChemicalReaction' object has no attribute 'GetReactingAtoms' == ERROR: test8Properties (__main__.TestCase) -- Traceback (most recent call last): File /home/chupvl/scisoft/rdkit/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py, line 286, in test8Properties self.failUnlessEqual(ps[0][0].GetAtomWithIdx(1).GetIsotope(),3); AttributeError: 'Atom' object has
Re: [Rdkit-discuss] RDKit ctest failed
The commands report following info (I recompiled to /home/chupvl/scisoft/RDKit_2012_06_1/ - this path). /home/chupvl/scisoft/RDKit_2012_06_1/rdkit/rdBase.so linux-vdso.so.1 = (0x7fff45a96000) libSmilesParse.so.1 = /home/chupvl/scisoft/RDKit_2012_06_1/lib/libSmilesParse.so.1 (0x7ff162648000) libSubstructMatch.so.1 = /home/chupvl/scisoft/RDKit_2012_06_1/lib/libSubstructMatch.so.1 (0x7ff162435000) libGraphMol.so.1 = /home/chupvl/scisoft/RDKit_2012_06_1/lib/libGraphMol.so.1 (0x7ff16212a000) libRDGeneral.so.1 = /home/chupvl/scisoft/RDKit_2012_06_1/lib/libRDGeneral.so.1 (0x7ff161ee9000) libRDBoost.so.1 = /home/chupvl/scisoft/RDKit_2012_06_1/lib/libRDBoost.so.1 (0x7ff161ce6000) libpython2.7.so.1.0 = /usr/lib/libpython2.7.so.1.0 (0x7ff1617c4000) libboost_python-py27.so.1.46.1 = /usr/lib/libboost_python-py27.so.1.46.1 (0x7ff161578000) libstdc++.so.6 = /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x7ff161278000) libm.so.6 = /lib/x86_64-linux-gnu/libm.so.6 (0x7ff160f7d000) libgcc_s.so.1 = /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x7ff160d67000) libc.so.6 = /lib/x86_64-linux-gnu/libc.so.6 (0x7ff1609aa000) libRDGeometryLib.so.1 = /home/chupvl/scisoft/RDKit_2012_06_1/lib/libRDGeometryLib.so.1 (0x7ff16078a000) libssl.so.1.0.0 = /lib/x86_64-linux-gnu/libssl.so.1.0.0 (0x7ff16052e000) libcrypto.so.1.0.0 = /lib/x86_64-linux-gnu/libcrypto.so.1.0.0 (0x7ff160166000) libz.so.1 = /lib/x86_64-linux-gnu/libz.so.1 (0x7ff15ff4e000) libpthread.so.0 = /lib/x86_64-linux-gnu/libpthread.so.0 (0x7ff15fd31000) libdl.so.2 = /lib/x86_64-linux-gnu/libdl.so.2 (0x7ff15fb2d000) libutil.so.1 = /lib/x86_64-linux-gnu/libutil.so.1 (0x7ff15f929000) /lib64/ld-linux-x86-64.so.2 (0x7ff162b87000) libDataStructs.so.1 = /home/chupvl/scisoft/RDKit_2012_06_1/lib/libDataStructs.so.1 (0x7ff15f64a000) Thank's! On Fri, Aug 17, 2012 at 1:42 PM, Greg Landrum greg.land...@gmail.comwrote: oops, hit send to soon. On Fri, Aug 17, 2012 at 7:38 PM, Greg Landrum greg.land...@gmail.com wrote: Dear Vladimir, On Fri, Aug 17, 2012 at 6:56 PM, Vladimir Chupakhin chu...@gmail.com wrote: I have added this into the .bashrc export RDBASE=/home/chupvl/scisoft/rdkit/ export PYTHONPATH=/home/chupvl/scisoft/rdkit/:/usr/include/python2.7/ export LD_LIBRARY_PATH=/home/chupvl/scisoft/rdkit/lib/ but actually received even more Failed messages. The error messages you are getting are strange and seem to be pointing to an older version of the RDKit being found. Could it be that you have either an older distribution somewhere or that you forgot to do make install after you built the code? you can check this by doing: ldd $RDBASE/rdkit/Chem/rdchem.so and: python -c 'from rdkit import rdBase; print rdBase.__file__' -greg -- Vladimir Chupakhin, Boston, MA, USA tel: +1-617-943-9710 LinkedIN: http://www.linkedin.com/in/chupvl -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
